BASIL Biochemistry Curriculum

This curriculum from the BASIL (Biochemistry Authentic Scientific Inquiry Laboratory) biochemistry consortium aims to get students to transition from thinking like students to thinking like scientists. Students will analyze proteins with known structure but unknown function using computational analyses and wet-lab techniques. BASIL is designed for undergraduate biochemistry lab courses, but can be adapted to first year (or even high school) settings, as well as upper-level undergraduate or graduate coursework. It is targeted to students in biology, biochemistry, chemistry, or related majors. Further details about the BASIL biochemistry consortium can be found on the BASIL blog.

The curriculum is flexible and can be adapted to match the available facilities, the strengths of the instructor and the learning goals of a course and institution. These lessons are often used as part of upper-level laboratory coursework with at least one semester of biochemistry as a pre-requisite or co-requisite. The lab has been designed for classes ranging from 10-24 students (working in teams of two or three) per lab section. This lesson can be adapted to laboratory courses for introductory biology, cell and molecular biology, or advanced biology labs.

Additional Information for Instructors

Additional information for instructors is available to registered university faculty. Learn more on our instructor information page.

If you use the resources from this page, please cite this work as:
McDonald AR, Bernstein HJ, Daubner SC, Goodman A, Irby SM, Koeppe JR, Mills JL, O’Handley SF, Pikaart MJ, Roberts RA, Sikora A, Craig, PA. BASIL Biochemistry Curriculum. https://basilbiochem.github.io/basil/, 2019.
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Acknowledgements

NSF logo

This work is supported by NSF IUSE 1503811, 1503699, 1502720, 1503676, 1503710, 1503798, 1503734, 1709170, 1709805, 1709592, 1710583, 1709355, 1709278, and 1710051.

The authors also wish to thank all of the faculty and students who have contributed to the development of the BASIL CURE curriculum.





This lesson is under development, please report issues to the GitHub repository

Modules

Introduction What is BASIL?
00:00 1. Structural Alignment with PyMOL and ProMOL How are PyMOL and ProMOL used to align active sites?
02:30 2. Protein BLAST Search How can similar protein sequences be identified using BLAST?
03:50 3. Using Pfam to Predict Protein Function How can a protein family be identified from its structure?
05:00 4. Structural Alignment with Dali How are similar protein structures identified?
07:00 5. Molecular Docking with AutoDock VINA and PyRx How is molecular docking used to screen for small molecule binding?
10:30 6. Expression of Proteins from Lactose-Inducible Vectors in E. coli How can bacteria be used to express a foreign protein?
19:00 7. Protein Purification How can an expressed protein be purified from a bacterial cell preparation?
24:45 8. Measurement of Protein Concentration How is concentration of protein in solution measured?
28:30 9. Using SDS-PAGE to assess the purification of protein How can SDS-PAGE assess the purity of a protein?
32:00 10. Protein Activity Assay What molecules can act as substrates for our protein of interest?
36:30 11. Enzyme Kinetics Assay How can quantitative values be obtained for an enzymatic reaction?
42:00 Finish

You may choose to use one or more modules in your course depending on your course objectives.